Seaweed feed offers a promising approach to enhance sustainability in aquaculture. While much research has focused on its effects on aquatic organisms, the impact of seaweed feed residuals on sediment carbon sequestration and bacterial community dynamics remains underexplored. This study aimed to address this gap through a 96-day incubation experiment using sediment from the coastal wetlands of Zhuhai in southern China. We evaluated the effects of seaweed feed derived from the red seaweed Gracilaria lemaneiformis by analyzing temporal changes in sediment physicochemical properties and microbial community dynamics. Our findings reveal that seaweed feed significantly improved sediment organic carbon and nitrogen storage (p <
0.01), enhanced the recovery of dissolved oxygen levels (p <
0.001) and bacterial α-diversity (p <
0.01) compared to normal feed. Additionally, the variability in microbial community structure (p <
0.01) and functional potential (p <
0.05) due to seaweed feed was less pronounced than that caused by normal feed. This reduced variability may result from the role of seaweed feed in stabilizing microbial community assembly, which helps mitigate fluctuations in bacterial structure and function. Overall, this study offers valuable insights for managing aquaculture ponds and coastal wetlands, contributing to the understanding of seaweed carbon sequestration and highlighting the potential of seaweed feed as a significant carbon sink beyond traditional cultivation practices.